Daniel A. Keedy

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Jane S. RichardsonProfessor of Biochemistry, Duke UniversityAdresse e-mail validée de duke.edu
David C. RichardsonProfessor of Biochemistry, Duke UniversityAdresse e-mail validée de kinemage.biochem.duke.edu
Jeff HeaddJohnson & Johnson Innovative MedicineAdresse e-mail validée de its.jnj.com
James S. FraserProfessor, University of California San FranciscoAdresse e-mail validée de ucsf.edu
Henry van den BedemSVP ML Research & Cheminformatics, Atomwise Inc. and Dept of BTS, UCSFAdresse e-mail validée de ucsf.edu
Bradley HintzeDuke UniversityAdresse e-mail validée de hintze.org
Paul D. AdamsLawrence Berkeley Laboratory & University of California BerkeleyAdresse e-mail validée de lbl.gov
Bruce DonaldProfessor of Computer Science, Mathematics, Chemistry, and Biochemistry, Duke UniversityAdresse e-mail validée de cs.duke.edu
James A. WellsUniversity of California, San FranciscoAdresse e-mail validée de ucsf.edu
T. Justin RettenmaierJnana TherapeuticsAdresse e-mail validée de jnanatx.com
Ivelin GeorgievVanderbiltAdresse e-mail validée de vumc.org
Rahel A. WoldeyesPostdoctoral Research Fellow - Stanford UniversityAdresse e-mail validée de stanford.edu
Lillian KennerAdresse e-mail validée de gene.com
David A. SivakProfessor and Canada Research Chair, Dept. of Physics, Simon Fraser UAdresse e-mail validée de sfu.ca
Matt Warkentinphysics, cornell universityAdresse e-mail validée de cornell.edu
Robert E. ThorneProfessor of Physics, Cornell UniversityAdresse e-mail validée de cornell.edu
David BakerUniversity of WashingtonAdresse e-mail validée de uw.edu
Yifan SongCyrus BiotechnologyAdresse e-mail validée de cyrusbio.com
Nicholas M PearceAssistant Professor, Linköping UniversityAdresse e-mail validée de liu.se
Mark HallenDuke UniversityAdresse e-mail validée de duke.edu

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Daniel A. Keedy

CUNY Advanced Science Research Center

Adresse e-mail validée de gc.cuny.edu - Page d'accueil

structural biology allostery protein design


Titre Trier par citations Trier par année Trier par titre	Citée par Citée par	Année
MolProbity: all-atom structure validation for macromolecular crystallography VB Chen, WB Arendall, JJ Headd, DA Keedy, RM Immormino, GJ Kapral, ... Biological crystallography 66 (1), 12-21, 2010	14886	2010
MolProbity: more and better reference data for improved all‐atom structure validation CJ Williams, JJ Headd, NW Moriarty, MG Prisant, LL Videau, LN Deis, ... Protein Science 27 (1), 293-315, 2018	3712	2018
Alternate states of proteins revealed by detailed energy landscape mapping MD Tyka, DA Keedy, I André, F DiMaio, Y Song, DC Richardson, ... Journal of molecular biology 405 (2), 607-618, 2011	397	2011
CryptoSite: expanding the druggable proteome by characterization and prediction of cryptic binding sites P Cimermancic, P Weinkam, TJ Rettenmaier, L Bichmann, DA Keedy, ... Journal of molecular biology 428 (4), 709-719, 2016	226	2016
Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography DA Keedy, LR Kenner, M Warkentin, RA Woldeyes, JB Hopkins, ... Elife 4, e07574, 2015	194	2015
An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering DA Keedy, ZB Hill, JT Biel, E Kang, TJ Rettenmaier, J Brandao-Neto, ... Elife 7, e36307, 2018	164	2018
Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR DA Keedy, H Van Den Bedem, DA Sivak, GA Petsko, D Ringe, MA Wilson, ... Structure 22 (6), 899-910, 2014	152	2014
osprey: Protein Design with Ensembles, Flexibility, and Provable Algorithms. P Gainza, KE Roberts, I Georgiev, RH Lilien, DA Keedy, CY Chen, F Reza, ... Methods in enzymology 523, 87, 2013	144	2013
Dead‐End elimination with perturbations (“DEEPer”): A provable protein design algorithm with continuous sidechain and backbone flexibility MA Hallen, DA Keedy, BR Donald Proteins: Structure, Function, and Bioinformatics, 2012	108	2012
Algorithm for backrub motions in protein design I Georgiev, D Keedy, JS Richardson, DC Richardson, BR Donald Bioinformatics 24 (13), i196-i204, 2008	100	2008
Ultrasonic characterization of human cancellous bone in vitro using three different apparent backscatter parameters in the frequency range 0.6-15.0 MHz BK Hoffmeister, DP Johnson, JA Janeski, DA Keedy, BW Steinert, ... IEEE transactions on ultrasonics, ferroelectrics, and frequency control 55 …, 2008	99	2008
The other 90% of the protein: Assessment beyond the Cαs for CASP8 template‐based and high‐accuracy models DA Keedy, CJ Williams, JJ Headd, WB Arendall III, VB Chen, GJ Kapral, ... Proteins: Structure, Function, and Bioinformatics 77 (S9), 29-49, 2009	98	2009
Exposing hidden alternative backbone conformations in X-ray crystallography using qFit DA Keedy, JS Fraser, H van den Bedem PLoS computational biology 11 (10), e1004507, 2015	92	2015
Conformational variation of proteins at room temperature is not dominated by radiation damage S Russi, A González, LR Kenner, DA Keedy, JS Fraser, H Bedem Synchrotron Radiation 24 (1), 73-82, 2017	63	2017
qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps GCP van Zundert, BM Hudson, SHP de Oliveira, DA Keedy, R Fonseca, ... Journal of Medicinal Chemistry 61 (24), 11183-11198, 2018	54	2018
Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place JJ Headd, RM Immormino, DA Keedy, P Emsley, DC Richardson, ... Journal of structural and functional genomics 10, 83-93, 2009	50	2009
Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B TS Mehlman, JT Biel, SM Azeem, ER Nelson, S Hossain, L Dunnett, ... Elife 12, e84632, 2023	48	2023
qFit 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle cryo‐EM density maps BT Riley, SA Wankowicz, SHP de Oliveira, GCP van Zundert, DW Hogan, ... Protein science 30 (1), 270-285, 2021	47	2021
737 Richardson JS, Richardson DC. 2010. MolProbity: all-atom structure validation for 738 macromolecular crystallography VB Chen, WB Arendall 3rd, JJ Headd, DA Keedy, RM Immormino, ... Acta Crystallogr D Biol Crystallogr 66, 12-21, 0	47*
Journey to the center of the protein: allostery from multitemperature multiconformer X-ray crystallography DA Keedy Biological Crystallography 75 (2), 123-137, 2019	37	2019

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